Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatttatccttatactggacatgaaaattaaacttaagtgattaataatgaatgaatgaataactatagtattcaatgttttgtgacttgattaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG

Basic information

species Glycine max
transcript GLYMA05G28260.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28260.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 2
----aatttatccttatactggacatgaaaattaaacttaagtgattaataatgaatgaatgaataactatagtattcaatgttttgtgacttgattaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG
    |  || |  || |     |  ||    | |   |    |    ||   |   |   ||   ||   |      | || | |||  |||||    || |||| ||||||||||| || ||||||  ||||||||| |||||||||||||| || |||||  ||||||| || || || || ||||| ||||| || |||||
cacaagcttttttttctctgctatgtgcttgtgatggtgggattgcaaaatctatttttctgttaaatgctcaccagctatttcttg-aacttgt---atccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG

upper sequence: GLYMA05G28260.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g28980.1 (Oryza sativa), 3'ss of exon 2
--aatttatccttatactggacatgaaaattaaacttaagtgattaataatgaatgaatgaataactatagtattcaatgttttgtgacttgattaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG
  ||| || ||    ||   |    | |||||      ||     | || | |   ||      | ||||   |  |   |  ||| |||   | | | |||| ||||| || ||||||||||||   || || || |||||||||||||||||||||||  ||||||| || || || ||  | || ||||| |||  |||
gcaatataaccaccaacaacatcatataattatga--gaggagggagtatttagcaaacagtatattataaggtaaatgatgatgttactctctaattacagGCCAAGTTATTAAGGGATGGGATTTGGGCATTAAGACCATGAAGAAAGGTGAGAATGCTATTTTCACCATTCCACCAGAGCTTGCATATGGTGAGGATGG

upper sequence: GLYMA05G28260.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 2
aatttatccttatactggacatgaaaattaaacttaagtgattaataatgaatgaatgaataactatagtattcaatgttttgtgact---tgattaatgc--agGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG
   | |    ||   |||| || |   |    ||    ||  |  |  |  |  | ||   |  |  |  ||  |||| |   | |||   |  | |||||  ||| |||||||||||||| |||||| |||| ||||| |||||||||||||| || |||||  |||| || || || || ||  ||||||||||||  |||||
--gtaaattctagcttggagatcatcctgtttctctcttgcctctttgttgac-attgccaagttgaaaaat--aatgctcattaactattttgtcaatgcccagGTCAAGTGATAAAGGGTTGGGATCAAGGAATCAAGACCATGAAGAAAGGAGAAAATGCTATTTTTACCATTCCTCCAGAGCTGGCTTATGGAGCATCTGG

upper sequence: GLYMA05G28260.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ06798 (Selaginella moellendorffii), 3'ss of exon 2
aatttatccttatactggacatgaaaattaaacttaagtgattaataatgaatgaatgaataactatagtattcaatgttttgtgacttgattaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG
                                         | |   |   ||| ||   || ||   || || | | || | |        |  || ||| ||||| || ||||||||||| ||||| || || || |||||||| |||||||| ||  | ||||| || |||||||  ||||||||||||||  ||||
----------------------------------------gtgagcgagttatggatttctatctg--gtgttgatttttctttcttcgtgcttgtgtagGCCAAGTTATCAAGGGATGGGACGAAGGCATTAAGACAATGAAGAAGGGTGAGAACGCGGTGTTCACCATTCCCCCGGCCTTGGCTTATGGAGAAGCTGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|213587010|gb|DB961747.1|DB961747
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAGAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|11274712|gb|BF325047.1|BF325047
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|193697925|gb|FK640592.1|FK640592
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|298186347|gb|HO036980.1|HO036980
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|209705418|gb|BW668037.1|BW668037
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|298165125|gb|HO011174.1|HO011174
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGA
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGA
EST: gi|192314623|gb|FK006381.1|FK006381
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|298175414|gb|HO015047.1|HO015047
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|298185757|gb|HO028068.1|HO028068
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|213608771|gb|DB962865.1|DB962865
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAGAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|5606078|gb|AI900176.1|AI900176
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|192314622|gb|FK006380.1|FK006380
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|298174862|gb|HO014779.1|HO014779
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|298186240|gb|HO036873.1|HO036873
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|209701585|gb|BW673110.1|BW673110
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
EST: gi|298183468|gb|HO028681.1|HO028681
EST:     TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAG                         GGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG
genomic: TGATTCTAGCCGCGATAGGGGCACCCCCTTCAAGTTCAAGCTAGGCCAAGgtacacattc ... attaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgaatgaatgaataactatagtattcaatgttttgtgacttgattaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG
             aataactatagtatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatttatccttatactggacatgaaaattaaacttaagtgattaataatgaatgaatgaataactatagtattcaatgttttgtgacttgattaatgcagGGCAAGTGATAAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCGGAATTGGCTTATGGAGAGTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - -atactgg
- - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg